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Crystal Structure of the Catalytic Core of an RNA Polymerase Ribozyme Complexed with an Antigen Binding Antibody Fragment
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6 277 Fab-RNA: 10 mM Tris pH 7.6, 20.1 mM MgCl2, 0.1 mM EDTA, 150 mM NaCl. Screen solution: 50 mM cacodylate pH 6.0, 20 mM NaCl, 1 mM CdCl2, 32% MPD. Cryo: Paratone-N, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 4.13 70.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 207.499 α = 90 b = 206.452 β = 90 c = 135.926 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD MARMOSAIC 300 mm CCD 2009-04-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D APS 21-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.1 50 98.2 0.155 6.1 6.7 52330
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.1 3.15 79.6 0.585 3.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3.1 50 52239 2648 98.2 0.208 0.207 0.225 0.224 RANDOM 68.09
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.79 -0.47 -0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.653 r_dihedral_angle_3_deg 14.239 r_dihedral_angle_4_deg 13.073 r_dihedral_angle_1_deg 4.76 r_angle_refined_deg 1.323 r_scangle_it 1.25 r_scbond_it 0.716 r_mcangle_it 0.41 r_mcbond_it 0.191 r_chiral_restr 0.058
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.653 r_dihedral_angle_3_deg 14.239 r_dihedral_angle_4_deg 13.073 r_dihedral_angle_1_deg 4.76 r_angle_refined_deg 1.323 r_scangle_it 1.25 r_scbond_it 0.716 r_mcangle_it 0.41 r_mcbond_it 0.191 r_chiral_restr 0.058 r_bond_refined_d 0.006 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6604 Nucleic Acid Atoms 5470 Solvent Atoms 104 Heterogen Atoms 37
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling